Yes, some of the claims that various firmwares have crashed the PS3 that turn up when the firmware is updated are likely a result of coincidence. However, in this case, the problem is definitely real. Here are a few points.
This problem occurs whether you have the update on memory stick, or HDD. The update is also in the correct directory, which is PS3\Update - and I've swapped my HD before, with no problem.
I myself did use Sony's backup facility. However, how do you get 2 HDs in a PS3? You can't - you have to put a new one in, and then use restore to put the old data back. However, the problem occurs before the PS3 even gets as far as the main menu. The PS3 requires the firmware to prepare the new HD to be used, and this is where the problem crops up.
It's not clear if this affects only Slims or Slims and fats. There have at least been one or two apparent reports people with Fat PS3s having the issue.
Putting the old HDD back in does mean the PS3 works - but I put the 3.41 firmware on just before I upgraded the HDD. I could kick myself.